Hi Martin, thanks a lot. Using export PKG_CFLAGS = '-I/usr/lib/jvm/java-6-sun-1.6.0.07/include -I/usr/lib/jvm/java-6-sun-1.6.0.07/include/linux' I was able to install RWebServices_1.6.0. I'll try the SVN versions of SJava and RWebservices. Thanks again for your help. Bastian -------- Original-Nachricht -------- > Datum: Mon, 15 Dec 2008 22:47:40 -0800 > Von: Martin Morgan <mtmorgan at="" fhcrc.org=""> > An: "Bastian Angermann" <angerb at="" gmx.de=""> > CC: bioconductor at stat.math.ethz.ch > Betreff: Re: [BioC] RWebServices installation > Hi Bastian -- > > "Bastian Angermann" <angerb at="" gmx.de=""> writes: > > > Hi List, > > > > I am trying to install RWebServices, but the installation fails > > because the jni.h include is not found by the c compiler. I have > > tried numerous variations of giving the option > > --configure-args,--configure-vars but these don't seem to have any > > effect since the parameter I provide to them is not passed on to the > > compiler. The java settings in R_HOME/etc/Makevars are set and > > point to the correct location but are not handed to the compiler > > either. How can I pass the appropriate CFLAGS to the installation > > procedure? > > The version of RWebServices available in R-2.8.0 does not understand > --configure-args, etc. Try > > PKG_CFLAGS=-I/usr/lib/jvm/java-6-sun-1.6.0.07/include > /home/bastian/RWebServices_1.6.0.tar.gz > > There's an updated version of SJava available via svn, at > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SJava > > and in general expect changes (for the better!) in both SJava at the > above svn and RWebServices as available in the bioc-devel repository. > > Please let me know how this goes. > > Martin > > > Thanks, > > Bastian Angermann > > > > This is the output of one of my installation attempts (I tried both sun > java 1.5 and 1.6) > > bastian at laptop1:~$ R CMD INSTALL -d > --configure- args='CFLAGS=-I/usr/lib/jvm/java-6-sun-1.6.0.07/include/' /home/bastian/RWebServices_1.6.0.tar.gz > > * Installing to library '/home/bastian//lib64/R/library' > > 'R CMD INSTALL': in startdir= /home/bastian with tmpdir= > /tmp/R.INSTALL.y12220 > > lib= '/home/bastian//lib64/R/library', pkgs= ' > "/tmp/R.INSTALL.y12220/RWebServices"' > > before checking lockdir= '/home/bastian/lib64/R/library/00LOCK' > > after checking lockdir > > build_help_opts= '--debug --txt --html --latex --example' > > 'R CMD INSTALL': now doing 'eval ... do_install': > > * Installing *source* package 'RWebServices' ... > > > > Guessing SJava home: /home/bastian/lib64/R/library/SJava > > > > configure: creating ./config.status > > config.status: creating inst/scripts/RWebServicesEnv.properties > > ** libs > > + mkdir -p /home/bastian/lib64/R/library/RWebServices/libs > > + test -f src/Makefile > > + cd src > > + ls RWebServicesConverters.c init.c *.cc *.cpp *.f90 *.f95 *.mm > > + srcs=init.c > > RWebServicesConverters.c > > + test -r Makevars > > + allfiles=init.c > > RWebServicesConverters.c > > + cd /home/bastian//lib64/R/bin/exec > > + ls > > + archs=R > > + R_ARCH_keep= > > + test -n init.c > > RWebServicesConverters.c > > + test -x ../configure > > + test -n > > + sh /home/bastian//lib64/R/bin/SHLIB -o RWebServices.so init.c > RWebServicesConverters.c > > gcc -std=gnu99 -I/home/bastian//lib64/R/include -I/usr/local/include > -fpic -g -O2 -c init.c -o init.o > > gcc -std=gnu99 -I/home/bastian//lib64/R/include -I/usr/local/include > -fpic -g -O2 -c RWebServicesConverters.c -o RWebServicesConverters.o > > RWebServicesConverters.c:1:17: error: jni.h: No such file or directory > > RWebServicesConverters.c: In function ?RCharScalar_JavaString?: > > RWebServicesConverters.c:26: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:26: error: (Each undeclared identifier is > reported only once > > RWebServicesConverters.c:26: error: for each function it appears in.) > > RWebServicesConverters.c:26: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:28: error: ?jobject? undeclared (first use > in this function) > > RWebServicesConverters.c:28: error: expected ?;? before ?value? > > RWebServicesConverters.c:34: error: ?value? undeclared (first use in > this function) > > RWebServicesConverters.c: In function ?RIntegerScalar_JavaInteger?: > > RWebServicesConverters.c:44: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:44: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:45: error: ?jclass? undeclared (first use > in this function) > > RWebServicesConverters.c:45: error: expected ?;? before > ?thisClass? > > RWebServicesConverters.c:46: error: ?jmethodID? undeclared (first > use in this function) > > RWebServicesConverters.c:46: error: expected ?;? before > ?thisConstructor? > > RWebServicesConverters.c:47: error: ?jobject? undeclared (first use > in this function) > > RWebServicesConverters.c:47: error: expected ?;? before ?value? > > RWebServicesConverters.c:50: error: ?value? undeclared (first use in > this function) > > RWebServicesConverters.c:50: error: ?thisClass? undeclared (first > use in this function) > > RWebServicesConverters.c:50: error: ?thisConstructor? undeclared > (first use in this function) > > RWebServicesConverters.c: In function ?RNumericScalar_JavaDouble?: > > RWebServicesConverters.c:61: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:61: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:62: error: ?jclass? undeclared (first use > in this function) > > RWebServicesConverters.c:62: error: expected ?;? before > ?thisClass? > > RWebServicesConverters.c:63: error: ?jmethodID? undeclared (first > use in this function) > > RWebServicesConverters.c:63: error: expected ?;? before > ?thisConstructor? > > RWebServicesConverters.c:64: error: ?jobject? undeclared (first use > in this function) > > RWebServicesConverters.c:64: error: expected ?;? before ?value? > > RWebServicesConverters.c:67: error: ?value? undeclared (first use in > this function) > > RWebServicesConverters.c:67: error: ?thisClass? undeclared (first > use in this function) > > RWebServicesConverters.c:67: error: ?thisConstructor? undeclared > (first use in this function) > > RWebServicesConverters.c: In function ?RLogicalScalar_JavaBoolean?: > > RWebServicesConverters.c:78: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:78: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:79: error: ?jclass? undeclared (first use > in this function) > > RWebServicesConverters.c:79: error: expected ?;? before > ?thisClass? > > RWebServicesConverters.c:80: error: ?jmethodID? undeclared (first > use in this function) > > RWebServicesConverters.c:80: error: expected ?;? before > ?thisConstructor? > > RWebServicesConverters.c:81: error: ?jobject? undeclared (first use > in this function) > > RWebServicesConverters.c:81: error: expected ?;? before ?value? > > RWebServicesConverters.c:84: error: ?value? undeclared (first use in > this function) > > RWebServicesConverters.c:84: error: ?thisClass? undeclared (first > use in this function) > > RWebServicesConverters.c:84: error: ?thisConstructor? undeclared > (first use in this function) > > RWebServicesConverters.c: In function ?RCharVector_JavaStringArray?: > > RWebServicesConverters.c:95: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:95: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:97: error: ?jstring? undeclared (first use > in this function) > > RWebServicesConverters.c:97: error: expected ?;? before ?str? > > RWebServicesConverters.c:98: error: ?jobject? undeclared (first use > in this function) > > RWebServicesConverters.c:98: error: expected ?;? before ?value? > > RWebServicesConverters.c:101: error: ?value? undeclared (first use > in this function) > > RWebServicesConverters.c:103: error: ?str? undeclared (first use in > this function) > > RWebServicesConverters.c: In function ?RList_JavaObjectArray?: > > RWebServicesConverters.c:116: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:116: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:118: error: ?jobject? undeclared (first use > in this function) > > RWebServicesConverters.c:118: error: expected ?;? before ?ele? > > RWebServicesConverters.c:119: error: expected ?;? before ?value? > > RWebServicesConverters.c:122: error: ?value? undeclared (first use > in this function) > > RWebServicesConverters.c:124: error: ?ele? undeclared (first use in > this function) > > RWebServicesConverters.c: In function ?RIntegerVector_JavaIntArray?: > > RWebServicesConverters.c:137: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:137: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:139: error: ?jintArray? undeclared (first > use in this function) > > RWebServicesConverters.c:139: error: expected ?;? before ?value? > > RWebServicesConverters.c:140: error: ?jint? undeclared (first use in > this function) > > RWebServicesConverters.c:140: error: ?els? undeclared (first use in > this function) > > RWebServicesConverters.c:141: error: ?jboolean? undeclared (first > use in this function) > > RWebServicesConverters.c:141: error: expected ?;? before > ?isCopy? > > RWebServicesConverters.c:144: error: ?value? undeclared (first use > in this function) > > RWebServicesConverters.c:145: error: ?isCopy? undeclared (first use > in this function) > > RWebServicesConverters.c: In function > ?RNumericVector_JavaDoubleArray?: > > RWebServicesConverters.c:159: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:159: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:161: error: ?jdoubleArray? undeclared > (first use in this function) > > RWebServicesConverters.c:161: error: expected ?;? before ?value? > > RWebServicesConverters.c:162: error: ?jdouble? undeclared (first use > in this function) > > RWebServicesConverters.c:162: error: ?els? undeclared (first use in > this function) > > RWebServicesConverters.c:163: error: ?jboolean? undeclared (first > use in this function) > > RWebServicesConverters.c:163: error: expected ?;? before > ?isCopy? > > RWebServicesConverters.c:166: error: ?value? undeclared (first use > in this function) > > RWebServicesConverters.c:167: error: ?isCopy? undeclared (first use > in this function) > > RWebServicesConverters.c: In function > ?RLogicalVector_JavaBooleanArray?: > > RWebServicesConverters.c:181: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:181: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:183: error: ?jbooleanArray? undeclared > (first use in this function) > > RWebServicesConverters.c:183: error: expected ?;? before ?value? > > RWebServicesConverters.c:184: error: ?jboolean? undeclared (first > use in this function) > > RWebServicesConverters.c:184: error: ?els? undeclared (first use in > this function) > > RWebServicesConverters.c:185: error: expected ?;? before > ?isCopy? > > RWebServicesConverters.c:188: error: ?value? undeclared (first use > in this function) > > RWebServicesConverters.c:189: error: ?isCopy? undeclared (first use > in this function) > > RWebServicesConverters.c: In function ?RRawVector_JavaByteArray?: > > RWebServicesConverters.c:203: error: ?JNIEnv? undeclared (first use > in this function) > > RWebServicesConverters.c:203: error: ?env? undeclared (first use in > this function) > > RWebServicesConverters.c:205: error: ?jbyteArray? undeclared (first > use in this function) > > RWebServicesConverters.c:205: error: expected ?;? before ?value? > > RWebServicesConverters.c:206: error: ?jbyte? undeclared (first use > in this function) > > RWebServicesConverters.c:206: error: ?els? undeclared (first use in > this function) > > RWebServicesConverters.c:207: error: ?jboolean? undeclared (first > use in this function) > > RWebServicesConverters.c:207: error: expected ?;? before > ?isCopy? > > RWebServicesConverters.c:210: error: ?value? undeclared (first use > in this function) > > RWebServicesConverters.c:211: error: ?isCopy? undeclared (first use > in this function) > > make: *** [RWebServicesConverters.o] Error 1 > > + has_error=true > > + chmod 755 /home/bastian/lib64/R/library/RWebServices/libs/* > > chmod: cannot access > `/home/bastian/lib64/R/library/RWebServices/libs/*': No such file or directory > > + cd .. > > + true > > + error compilation failed for package 'RWebServices' > > + echo ERROR: compilation failed for package 'RWebServices' > > ERROR: compilation failed for package 'RWebServices' > > + do_exit_on_error > > + remove_R_package_dir=yes > > + test -n /tmp/R.INSTALL.y12220/RWebServices > > + get_dcf_field Contains /tmp/R.INSTALL.y12220/RWebServices/DESCRIPTION > > + ws=[ ] > > + /bin/sed -n /^Contains:/,/^[^ ]/p > /tmp/R.INSTALL.y12220/RWebServices/DESCRIPTION > > + /bin/sed -n 1s/^Contains:[ ]*//p; /^[ ]/p > > ]*$//n/sed /^[ ]/s/^[ ]*//; s/[ > > + bundlepkg= > > + test -z > > + bundlepkg=RWebServices > > + false > > + pkgdir=/home/bastian/lib64/R/library/RWebServices > > + test yes = yes > > + test -n /home/bastian/lib64/R/library/RWebServices > > + message Removing '/home/bastian/lib64/R/library/RWebServices' > > + echo ** Removing '/home/bastian/lib64/R/library/RWebServices' > > ** Removing '/home/bastian/lib64/R/library/RWebServices' > > + rm -rf /home/bastian/lib64/R/library/RWebServices > > + test -n RWebServices > > + test -d /home/bastian/lib64/R/library/00LOCK/RWebServices > > + do_cleanup > > + do_cleanup_tmpdir > > + cd /home/bastian > > + test -d /tmp/R.INSTALL.y12220 > > + rm -rf /tmp/R.INSTALL.y12220 > > + test yes = no > > + true > > + rm -rf /home/bastian/lib64/R/library/00LOCK > > + exit 1 > > > > -- > > Sensationsangebot verl?ngert: GMX FreeDSL - Telefonanschluss + DSL > > f?r nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Sensationsangebot verl?ngert: GMX FreeDSL - Telefonanschluss + DSL f?r nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a -- Sensationsangebot verl?ngert: GMX FreeDSL - Telefonanschluss + DSL f?r nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a